maki

Hi Brian, Thank you for your quick reply. According to your advice and the example in Section 5.2 of the Guide, I have carried out new trials like the attached file. Thanks to your kind explanation, the calculations came to be converged. However, unfortunately, biomass of Aerobe-2 doesn’t increase, yet. I’m a complete novice about the BASIC language. I have no idea whether my input is correct or not, and what is wrong concerning my custom rate law script. Could you check them? ------------- aff = QoverK * exp(-ATP_number * ATP_energy / (8.3143 * TK)) aff = aff^order1 IF (aff > 1.0) THEN aff=1.0 prod = 1.0 prodKd1 = KD prodKd2 = 1.0 prodKa1 = KA prodKa2 = 1.0 tpf = 1.0 - aff fd = prodKd2 / (prodKd1 + prodKd2)^PKD fa = prodKa2 / (prodKa1 + prodKa2)^PKA setgwbvar("TPF", tpf) setgwbvar("FD", fd) setgwbvar("FA", fa) setgwbvar("biomass", biom) biomass0 = 1.0 rate = rate_con * biomass * FD * FA * TPF IF (Deltat <= 0.0) THEN GOTO end_block rate0 = dndt0/(biomass0 * Wmass) rpave = (1.0-Theta)*rate0 + Theta*rprime biom = biomass0*exp((growth_yield*rpave-decay_con)*Deltat) IF biom < 0.0 THEN biom = 0.0 end_block: return rate * biomass * Wmass IF molality ("Acetate") < 0.0001 THEN 20 ELSE 40 20: rate = rate_con * biomass * FD * FA * TPF GOTO 60 40: rate = 0 60: RETURN rate ------------- Best regards, Maki Acetate_v3.txt Custom_rate_law_trial3.rea

Hi Brian, Thank you for working on the problems. I would appreciate if you could let me know how things are coming along. Or, if you don’t mind, could you indicate a successful example including the microbial kinetics with custom rate law similar with my post? I would like to know whether it’s due to my input or not. Best regards, Maki

Hi Brian, Thank you for your consideration. It will be grateful if the two problems (convergence of calculation and the script editor) are fixed very soon. Best regards, Maki

Hi Brian, Thank you for your reply and letting me know the same phenomenon. You pointed out as below. > When I open your script none of the kinetic parameters (rate constant, initial biomass, etc.) for microbe-Aerobe-2 have been assigned a value. That phenomenon is just what I wanted to show you. This time, I attached four kinds of React file concerning custom rate law. 1. Crl01_ori.rea: The original file without using custom rate law. 2. Crl02_script.rea: The file set with script setting of custom rate law. 3. Crl03_command.rea: The file set with command of custom rate law. 4. Crl04_script_file.rea: The file set with script file of custom rate law. In addition above files, I attached the illustration of their explanation. I attached Crl02 I have already set the custom rate law using script editor. So, you can see the same phenomenon with previous post. When you try to carry out Crl02 again, please write the custom rate law script of the previous post in the Field variable script of script editor. When you try to carry out Crl04, please convert ‘.txt’, extension of my attached script file ‘Acetate.txt’, to ‘.bas’ for reading in React, and please select the bas file by yourself again, in the rate law setting on the Reactants pane. As you know, the directories in your computer and mine are different from each other. The results of my trial were as follows: Crl01 converged. Calculations of Crl02 and Crl03 didn’t start. Calculation of Crl04 file stopped just before the threshold set by custom rate law. I need your help about two problems I have. First: I would like to know how to make calculation of microbial kinetics with custom rate law converge. Even if I change parameters, values, and their possible combinations, the calculation stopped just before threshold set by custom rate law in all cases. For example, I tried to change species, threshold value, equation of rate in line 20, not 0 but 1e-20 in line 40, and so on. As you know, I have also tried other kinds of microbe. Second: If possible, I would like to practically use Crl02 or Crl03 because of needless to refer to an external file. I wonder that my inputs are incorrect in Crl02 and Crl03. Could you revise my inputs to improve Crl02 and Crl03? If my explanation is not enough yet, please let me know. Thank you for reading this long post and being patient with my English. Best regards, Maki Crl01_ori.rea Crl02_script.rea Crl03_command.rea Crl04_script_file.rea Acetate.txt

Hi I have been trying to calculate microbial kinetics using custom rate law (script and script file). According to the support’s advice, I started to try it under simpler setting. I assumed that two kinds of aerobe utilized different electron donors. Kinetics settings were the same for paying attention to apply custom rate law of Aerobe-2. Custom rate law in script or script file was set based on the support’s advice as below. I also assumed that when ‘Acetate’ used by Aerobe-1 become below 0.0001, Aerobe-2 start the reaction. The bas file was converted to text file and attached. IF molality ("Acetate") < 0.0001 THEN 20 ELSE 40 20: rate = rate_con * biomass * FD * FA * TPF GOTO 60 40: rate = 0 60: RETURN rate In spite of various trials, the calculations stopped just before reaching 0.0001 in the concentration of 'Acetate' and never converged in all cases. How should I handle this problem concerning the custom rate law? In addition, when the React program with custom rate law in ‘script’ editor of the Reactants pane is closed, and opened again, equations of ‘script’ showed the irregular description and brought an error. Could you check the problem, too? Best regards, Maki Custom_rate_law_trial2.rea Acetate.txt

Hi Brian, Sorry for delay reply. I understand that “Master Eh” (O2(aq), Eh, pe) constrains coupled redox pairs only. On the other hand, what decides “Master Eh” after reaction? In many cases, “Master Eh” seems to have equaled to “Eh (O2(aq)/H2O)” in the Xtplot and Gtplot even if any or no redox couples are decoupled. Does this fact mean that although “Master Eh” in GWB constrains the distribution of oxidant and reductant in each of redox pairs, the distribution of oxidant and reductant in each of redox pairs doesn’t control “Master Eh” even after kinetic reaction is carried out, and only “Eh (O2(aq)/H2O)” is cosidered in “Master Eh”? If I set the kinetic sulfate reduction (Acetate + SO4-- -> 2*HCO3- + HS-) under the condition which O2(aq) concentration is given and I don’t decouple HS-/SO4--, is “Master Eh” calculated by considering “Eh(HS-/SO4--)”? Though I can track the Eh of the redox pairs that I am interested in as you suggested, can I track “Master Eh” which is calculated based on redox pairs? If my explanation is not clear, could you let me know? Best regards, Maki

Thank you for your detailed reply. 1. I’m complicated with the problem in relation to decoupling of redox pair and Basis setting. I understand that decoupled redox pair is considered separately from the “Master Eh”. In the case, however, I think that users cannot set the related Basis (for example Lactic_acid(aq)) for microbial kinetics in the initial system. How do I handle their setting in the case that I would like to set the microbial kinetics and I would like to consider electron donor or acceptor for Master Eh value at the same time? Or should I adopt the Eh value of specific redox couple (Eh(Lactic_acid(aq)/Methane(aq)) in my example) as Master Eh? 2. I have tried the rate law script as below. IF molality ("O2(aq)") > 0.00001 THEN 20 ELSE 40 20: rate = 0.0 GOTO 60 40: rate = rate_con * biomass * FD * FA * TPF 60: RETURN rate Unfortunately, the calculation didn’t converge with the message “N-R didn't converge after 400 its., maximum residual = 3.97e+119, Xi = 0.0243”. Even if I exchanged the value of O2(aq) molality many times, neither that worked. If the script or input values has any problem, could you point out it? Best regards, Maki

Hi Using GWB software, I’m trying to reproduce the in-situ transition of functional microbial communities with thermodynamic ladder. According to the existing advices in this forum, I have started trial under the simplified condition. I attached the React file for the trial. The main concept of the trial is to reproduce the decrease of Eh with consumption of O2(aq) by aerobes in closed chamber. Next is that carbonate and hydrogen are used as resources for hydrogenotrophic methanogenesis. Analysis time was basically for 5 days (besides, 1 day, 5 month, and so on). Thermo.com.V8.R6+.dat was used with the decoupling of Lactic_acid(aq)/HCO3-, H2(aq)/H+, and Methane(aq)/HCO3-.. Lactic_acid(aq) was swapped to Lactate. Results were as below: - The decrease of Eh was not observed in the result of the above simulation although O2(aq) concentration and Lactic_acid(aq) concentration decreased until zero with the increase of Aerobe biomass. Rather, the Eh acutely increased. - Though HCO3- and H+ were provided to the system, they seemed to be used by methanogen. I have several questions. Concerning the decrease of Eh in the system and the consistency between change of Eh and methanogenesis. -Q1. I think that the ‘Eh’ in the Gtplot seems to reflect ‘Eh(O2(aq)/H2O)’ only, without reflecting other redox couplings, for example ‘Eh(H+/H2(aq)’, ‘Eh(Lactic_acid(aq)/Methane(aq)’, and so on. I hope to express the anaerobic condition (around -250 mV) for methanogenesis after O2(aq) is completely consumed. How should I revise the React setting? In addition, what does the ‘Eh’ in the Gtplot represent? Mixed potential or Eh(O2(aq)/H2O) only? -Q2. I expect that the methanogenesis which needs extremely low Eh (around -250 mV) starts after all of O2 is consumed. However, methanogen didn’t start after O2 consumption in the simulation. On the other hand, when I input larger value of H2(aq) (ex. 1e-5), methanogenesis have started in spite of the fact that there remained O2(aq) in the system and Eh value was so high (around +700 mV). Could anyone give me advices regarding the decrease of Eh in the system and the consistency between change of Eh and methanogenesis? -Q3. In this case, can the helper function in rate law option on the Kinetic microbe-Aerobe be available for solving this problem? If so, could you give me any example of rate raw available for this case? Concerning the consumption of H2(aq) or H+. -Q4. Hydrogenotrophic methanogenesis is shown by the equation as below. HCO3- + 4*H2(aq) + H+ -> Methane(aq) + 3*H2O However, hydrogen released from Aerobic respiration seems not to be used in methanogenesis in the simulation. Because H+ in fluid didn’t decrease and H2(aq) concentration was constant for any analysis time. Of course, biomass of methanogen decreased according to only decay constant. Even if I set hydrogen of equation by unifying in either H2(aq) or H+ in the all kinetics for microbes, it results in charge imbalance. How should I handle Basis and Reactants to describe hydrogenotrophic methanogenesis? Thank you for your consideration. Best regards, Maki O_Me1_simplified.rea

Hi, Brian Thank you for the maintenance information. I'm glad to hear that. Best regards, Maki

Hi Brian, Thank you for your reply. Q1 When Edit -> Copy on the Color Map View with Variable type ‘Components in fluid’ and Variable units ‘mol/l’ after calculation is carried out, the values of text table pasted on excel file etc. shows 1.0000000385. I understand the explanation about the difference between free and bulk. And I’ll try to calculate the component concentration according to your suggestion. On the Color Map View with Variable type ‘Components in fluid’, Cl- values were like below. Variable units mol/l -> 1 molal -> 1.019 mol/kg -> 0.9621 In the case of Variable type ‘Species concentrations’, they were like below. mol/l -> 0.9899 molal -> 1.009 mol/kg -> 0.9524 I understand the difference between the case of mol/l and molal by above advice. However, why is the value in molal different from that in mol/kg? Doesn’t ‘molal’ represent 'mol/kg' in GWB software? If I have misunderstanding, could you let me know? Thank you for your consideration concerning Q2 and second question for Q1. Best regards, Maki

Hi, I have two questions. Q1. I have attached the X2t trial file which condition was so simplified. I have found that the values of Aqueous species on the X2t_output are different from the values of the species in fluid gained from the Map View of Xtplot after calculation of ‘Go Initial’. My Input value of Cl- is 1 mol/L in all nodes. The value of Cl- on X2t_output.txt is 1.009 mol/L in all nodes. The value of Cl- on the Map View of Xtplot is 1.0000000385 mol/L in all nodes. Which value is correct? I’m afraid that many a small error makes a big difference later. I guess that the difference between input and initial values is brought from equilibrium calculation under the input values. On the other hand, I have no idea of the difference between the values of X2t_output.txt and the Map View of Xtplot. I think my understanding about output of results is not adequate. Could anyone give me any advice? Q2. When ATP number is input on the microbial kinetics of Reactants pane, is the value (1) the number of proton per 1 molar of substance, (2) the total number of proton included in substance per the reaction, or (3) the total number of proton per the electron acceptor? For example, in the former reaction of denitrification as below, I assume that the produced ATP number per proton is one. 5*C3H5O3- + 12*NO3- + 2*H+ In this case, which is correct, (1) 5, (2) 25, or (3) 25/12 ? As with ATP number, how about stoichiometric number χ? If there is any rule to input their values considering molar number, could you tell me that? Best regards, Maki Q_different_values.x2t

Hi Brian, I understand the current state of the way to input discharge. Thank you for your reply. Best regards, Maki

Hi, I’m using X2t. I’m trying to import the flow field calculated by other program to X2t. I tried to use the node-by-node setting for X and Y discharges on the ‘flow field’ of the Domain pane. However, input values were not reflected in the results. I know that the GWB Reactive Transport Modeling Guide (p10 and p62) shows the values for discharges are indexed according to the nodal block boundary. On the other hand, if possible, I would like to import the flow field to ‘node block’ by using the node-by-node setting, not ‘nodal block boundary’. I think the node-by-node setting for the discharge as above will help me so much. In this case that input values were not reflected in the results, is there any problem node-by-node editor yet? Or, is the node-by-node setting for the discharge originally unavailable? Or, is the table of node-by-node setting lacking required another column and another line? Best regards, Maki

Hi Brian, I understand the procedure to show the TDS circles through the GSS spreadsheet. It works as you said. Many thanks, Maki

Hi, I’m using SpecE8 to evaluate the equilibrium state of aqueous species. In the Gtplot output after SpecE8 was carried out, TDS Circles is not shown, even in using example scripts of GWB. “TDS Circles” in the "View" is checked, "Data markers" are plotted, and “Show TDS as circles” window in the parameter setting for some diagrams which can express TDS circle is not activated (semi-transparent). Although I use the updated GWB (ver. 9.0.5), I’m not sure whether TDS circle is correctly shown in ver. 9.0.3, and whether the procedure to show the circle is wrong. Could anyone tell me how to indicate the TDS circles? Best regards, Maki

Hi Brian, Thank you for your pointing out. The matter concerning in-line table setting was cleared up by adding the vertical separators to corresponding lines. I appreciate for your understanding and cooperation. Best regards, maki

Hi Brian, Thank you for your quick action. I await good news about the fix of the importing flow field option. Best regards, maki

Hi Brian, Thank you for your advice. I became able to set the heterogeneous field by using a table file according to your advice and Appendix: Heterogeneity of Reactive Transport Modeling Guide. On the other hand, in-line table setting on Command pane didn’t work. The values of bottom line seem to constrain upper values to be same, just like node-by-node setting. For example, {1 1 1 2 0 2 2 0 2} in the command changed into {1 1 1 1 1 1 1 1 1} in the initial. For the time being, I will use a table file to set the heterogeneous field. It would be great if you could also resolve this matter soon. Best regards, maki

Hi Brian, Thank you for your reply. Although I have also tried to set the heterogeneity using “discharge” command on Command pane, the same errors have appeared again. As you said, I understand that there seems to be the problem with importing flow field option. Please forgive me for disturbing you with this matter, but I will be grateful for your understanding in dealing with these matters promptly, in a few weeks at the latest, if possible. Or, are there any alternative measures to set the heterogeneity of discharge under the present situation before the maintenance is done? Thank you for your special consideration. Best regards, maki

Hello, I’m trying to set heterogeneous values in Initial pane and Reactants pane of X2t. Although constant values are set with no problem, values set by node-by-node have not been correctly reflected in the result of time ‘0’. I show the examples of the heterogeneous setting in 3×3 domain to you. Case1 Correctly reflected case is as below. 2 1 2 2 1 2 2 1 2 Case2 The case incorrectly reflected is as below. 2 2 2 2 1 2 2 2 2 In this case, the result of time ‘0’ is as below. The value in the middle is 2, not 1 in input. 2 2 2 2 2 2 2 2 2 When the heterogeneity becomes more complicated, many unreflected cases appear. I wonder if this phenomenon happens on me only. In any case, could anyone tell me how to resolve this problem? Attached X2t file includes the node-by-node settings in CH3COO- of Initial pane and in initial biomass of Reactants pane. Thank you for your consideration. Best regards, maki

Hi, I have two questions. Q1. According to the section 4.4 Importing the flow field (p.61) of Reactive Transport Modeling Guide, I’m trying to import the flow field calculated by other program to X2t as initial values. However, it doesn’t work. When I pull down the menu of X and/or Y discharge in the setting field of ‘imported’ on the Domain pane and choose ‘table file’, the error massage has appeared as below: Error: Entry file_table is not a number or valid keyword. It is also the case of the other menus. If I only choose the ‘random’, ‘Error: Entry stddev is not a number or valid keyword’. ‘table file’, then, ‘Error: Entry file_table is not a number or valid keyword’. ‘equation’, then, ‘Error: equ is not a number or valid keyword’. ‘script file’, then, ‘Error: Entry file_script is not a number or valid’. ‘function’, then, ‘Error: Entry file is not a number or valid keyword’. ‘node by node’, then, ‘Error: Entry table is not a number or valid keyword’. ‘script’, then, ‘Error: Entry script is not a number or valid keyword’. I have no idea to resolve this problem. Could you tell me how to deal with this problem? Q2. In addition, I tried to set discharge x = 2 m/yr, y = 2 m/yr in the example of p.62 of Reactive Transport Modeling Guide. The Guide says that flow moves diagonally from the lower right to upper left of the domain as a result of the example run. In this case, is the corrected ‘from the lower left to upper right’? Best regards, maki

Hi Brian, Thank you for your reply. I think I understand the concept of promoting/inhibiting species in the case of a first-order rate law and a zero-order rate law, thanks to the explanation using the Michaelis-Menten equation. On the other hand, I don’t understand how to set the powers concretely, yet. After I do several trials of the REACT simulation, I want to ask you the concerning questions as a new topic in Forum. Thank you for your courteous response to my basic questions. Best regards, Maki

Hi Brian, Thank you for your detailed explanation. I understand as follows: Setting promoting and inhibiting species by inputting “apower” or “mpower” in the React means to vary the reaction rate (by catalyzing and impeding formation of the activated complex (Chapter 16)) according to the species concentration. If the promoting/inhibiting species is set to H+ by Custom rate law, it means that the reaction rate depends on pH. Do I understand what you mean? I have a further question. At the beginning of your previous reply, you said that rate laws are typically derived to fit experimental data. The examples in Chapter 16 use two kinds of exponent (1 for pH<1.5, and -1/2 for pH>8) in the term of activity (“H+”). Should I arbitrarily set the promoting/inhibiting species and their exponent (positive or negative) for fitting the experimental data to the simulation value and for reproducing in-situ data on the simulation? Regarding arbitrary setting of the exponents, is the same concept (to fit experiment data to the simulation) applied to ω and Ω in the case of Q/K? Best regards, Maki

Hi Brian, Thank you for quick reply and very useful advice. According to your advice, I will try to set the Custom rate law for expressing the sensitivity to pH in each of microbial communities. On the other hand, I have another question regarding the rate law. As you said, kinetics of dissolution and precipitation of albite are written in Chapter 16. If the sensitivity to pH using the Custom rate law is explained, I think that the inputs of promoting species (eq. 16.4) are not needed, furthermore, the exponent P for higher pH (eq. 16.6), neither. Are the promoting species and apower (H+) arbitrarily needed for calculating smoothly? Or, is there any inevitability? Best regards, Maki

Hi, I hope to express the biomass variation considering the sensitivity to pH. For example, a certain microbial community in the pyrite rock under the reductive condition decreases by acidification with progress of pyrite oxidation after boring. In contrast, acidophilic iron-oxidizing community increases under the low pH condition. Can I set the rate constant depending on the variation of the calculated pH and so on? Is there any other way to express it? Best regards, Maki